I have a dataset that is the result of differential expression analysis using DESeq and I want to figure out what gene ontology terms are enriched in the different conditions. The bacteria is not lab e coli, but a fairly common bacteria with a complete genome including refseq IDs and protein_IDs. I even downloaded the gene ontology terms for each protein. How would I go about figuring out enrichment of any terms given this data? I have never really worked with bacteria before.
As long as you have your GO terms assigned to the sequenced transcripts, it doesn't matter if it is bacteria or any other organism. You can use topGO in R, I find it highly useful, and as you work with DESeq you are bound to use R, so it fits nicely. Below you will find a link to a pdf file where its installation and usage are described.
https://bioconductor.org/packages/release/bioc/vignettes/topGO/inst/doc/topGO.pdf
Best regards,
Marcin
You may use the Cytoscape software and analyze your data with ClueGo app.
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